Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis
A meta-QTL analysis was conducted in Indian mustard to identify robust and stable meta-QTLs (MQTLs) by utilizing 1504 available QTLs, which included 891 QTLs for yield-related traits and 613 QTLs for quality traits. For yield-related traits, a total of 57 MQTLs (YRTs_MQTLs) were uncovered from the c...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/10/2442 |
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| author | Rahul Kumar Dinesh Kumar Saini Mukesh Kumar Veerala Priyanka Javed Akhatar Deepak Kaushik Amit Sharma Parmdeep Singh Dhanda Prashant Kaushik |
| author_facet | Rahul Kumar Dinesh Kumar Saini Mukesh Kumar Veerala Priyanka Javed Akhatar Deepak Kaushik Amit Sharma Parmdeep Singh Dhanda Prashant Kaushik |
| author_sort | Rahul Kumar |
| collection | DOAJ |
| description | A meta-QTL analysis was conducted in Indian mustard to identify robust and stable meta-QTLs (MQTLs) by utilizing 1504 available QTLs, which included 891 QTLs for yield-related traits and 613 QTLs for quality traits. For yield-related traits, a total of 57 MQTLs (YRTs_MQTLs) were uncovered from the clustering of 560 projected QTLs, which had a 4.18-fold smaller confidence interval (CI) than that of the initial QTLs, whereas, for quality traits, as many as 51 MQTLs (Quality_MQTLs) were derived from 324 projected QTLs, which had a 2.65-fold smaller CI than that of the initial QTLs. Sixteen YRTs_MQTLs were observed to share chromosomal positions with 16 Quality_MQTLs. Moreover, four most promising YRTs_MQTLs and eight Quality-MQTLs were also selected and recommended for use in breeding programs. Four of these selected MQTLs were also validated with significant SNPs that were identified in previously published genome-wide association studies. Further, in silico functional analysis of some promising MQTLs allowed the detection of as many as 1435 genes, which also involved 15 high-confidence candidate genes (CGs) for yield-related traits and 46 high-confidence CGs for quality traits. After validation, the identified CGs can also be exploited to model the plant architecture and to improve quality traits through marker-assisted breeding, genetic engineering, and genome editing approaches. |
| first_indexed | 2024-03-09T20:53:15Z |
| format | Article |
| id | doaj.art-22dfeb3aaaf349c294a3b703507ef89b |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T20:53:15Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-22dfeb3aaaf349c294a3b703507ef89b2023-11-23T22:27:15ZengMDPI AGAgronomy2073-43952022-10-011210244210.3390/agronomy12102442Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL AnalysisRahul Kumar0Dinesh Kumar Saini1Mukesh Kumar2Veerala Priyanka3Javed Akhatar4Deepak Kaushik5Amit Sharma6Parmdeep Singh Dhanda7Prashant Kaushik8Department of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, Punjab, IndiaDepartment of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, IndiaDepartment of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, Punjab, IndiaDepartment of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, Haryana, IndiaDepartment of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, Haryana, IndiaDepartment of Biochemistry, Punjab Agricultural University, Ludhiana 141027, Punjab, IndiaInstituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, SpainA meta-QTL analysis was conducted in Indian mustard to identify robust and stable meta-QTLs (MQTLs) by utilizing 1504 available QTLs, which included 891 QTLs for yield-related traits and 613 QTLs for quality traits. For yield-related traits, a total of 57 MQTLs (YRTs_MQTLs) were uncovered from the clustering of 560 projected QTLs, which had a 4.18-fold smaller confidence interval (CI) than that of the initial QTLs, whereas, for quality traits, as many as 51 MQTLs (Quality_MQTLs) were derived from 324 projected QTLs, which had a 2.65-fold smaller CI than that of the initial QTLs. Sixteen YRTs_MQTLs were observed to share chromosomal positions with 16 Quality_MQTLs. Moreover, four most promising YRTs_MQTLs and eight Quality-MQTLs were also selected and recommended for use in breeding programs. Four of these selected MQTLs were also validated with significant SNPs that were identified in previously published genome-wide association studies. Further, in silico functional analysis of some promising MQTLs allowed the detection of as many as 1435 genes, which also involved 15 high-confidence candidate genes (CGs) for yield-related traits and 46 high-confidence CGs for quality traits. After validation, the identified CGs can also be exploited to model the plant architecture and to improve quality traits through marker-assisted breeding, genetic engineering, and genome editing approaches.https://www.mdpi.com/2073-4395/12/10/2442meta-QTL analysisyield-related traitsquality traitsexpression analysiscandidate genes |
| spellingShingle | Rahul Kumar Dinesh Kumar Saini Mukesh Kumar Veerala Priyanka Javed Akhatar Deepak Kaushik Amit Sharma Parmdeep Singh Dhanda Prashant Kaushik Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis Agronomy meta-QTL analysis yield-related traits quality traits expression analysis candidate genes |
| title | Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis |
| title_full | Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis |
| title_fullStr | Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis |
| title_full_unstemmed | Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis |
| title_short | Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [<i>Brassica juncea</i> (L.) Czern. and Coss.] Using Meta-QTL Analysis |
| title_sort | revealing the genetic architecture of yield related and quality traits in indian mustard i brassica juncea i l czern and coss using meta qtl analysis |
| topic | meta-QTL analysis yield-related traits quality traits expression analysis candidate genes |
| url | https://www.mdpi.com/2073-4395/12/10/2442 |
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